Dear Dr. Darden,
Thanks for your mail. I am working on it.
Meanwhile I tried to do a simulation with ONLY the WATBOX216.
I am getting the error message
parameter skinnb+cutoffnb has value 0.10+02
the legal range is 0 to 0.98667E+01
Which is the similar message I got when I tried to use 32 water
molecules.
I don't want to play with ewald parameters without knowing. Could you
please tell me how to change those?
Also, a general question- how to generate box of waters (and only
waters) of different numbers (32,256,512,1024 so on) in AMBER? I was
using one water molecule as solute and then WATBOX216 but the structures
are taking very long time to equilibrate. Is there a better way?
thanks.
Pradipta
----- Original Message -----
From: darden <darden.gamera.niehs.nih.gov>
Date: Wednesday, September 17, 2003 8:29 am
Subject: Re: AMBER: MD problem!
> Dear Pradipta
> Its hard to tell without more info. However as a general policy,
> its best
> to first minimize to relieve bumps (with a new box you can have
> collisions
> across the box boundary), then run constant temperature to get up
> to 300K,
> then run (using a restart from the constant temp run) constant
> pressure to
> get up to correct density. You could for example run ~100 steps
> conjugate gradient minimization (keep shake on if you like although
> this
> will prevent minimization to a tight minimum--its ok you just want
> to
> relieve bumps). Next run NVT for ~10-20ps with default temperature
> control, this will get you to room temperature and listtot will not
> change
> much. Finally turn on NPT and run for ~10-20ps to get density
> right.
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Received on Thu Sep 18 2003 - 18:53:02 PDT
